i think the craft antagonists are the best. im stuck between L from Death Note and Izaya Orihara. they are just both stealthy and fuckin' too smart. i think that all anime fans know that if an anime antagonist and protagonist were to team up they would be unstoppable.

if L and light were to team up... they would be the best detectives on earth. and they wouldnt go crazy like light did because they would balance each other.

even though most people wouldnt pair them together, mikado is the main protagonist of durarara and if him and izaya were to team up, i think izaya would use some jedi mind trick to get mikado to have the dollars kill shizuo and then give the dollars to him.

Lordgenome probably.
I loved that he was completely an antagonist, yet, wasn't entirely evil, at least not from the get go. He was a hero who time twisted until his ideals and his mission and his whole being became vile. Anti-spiral runs by the same rule, but Lordgenome was more detestable, more relatable because he used to be human.

After those two, Magi's Mogamett probably, for similar reasons. Though I'm not really sure he counts so much as an antagonist. He's really more of an undesirable neutral, not really siding with Soloman or the Al Thamen, never really stood in Aladdin's way, just really a terrible, warped ruler. The discussions about discrimination, castes, and hedonism that his appearance sparked were amazing. There's a lot of manga with violence and nudity and extreme gore and all that, but I don't think I've seen many publishing on topics with this sort of gravity.

Not a very good picture, but this guy:
His name is 'The Claw', and he's from the anime Gun X Sword. He actually tries to make convincing arguments to the protagonist, rather than use the normal stuff a lot of other anime villains do. He's a villain you sympathize yet disagree with, and yet, you don't pity him at all.

I guess he gets props from me because as said, he's different from your normal sort of villain.